Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below).

• Version: 0.14.0
• Added: November, 2018
• Updated: February, 2023
• Link: https://github.com/jts/nanopolish

See versions which are available:

$ module avail nanopolish

Load one version into your environment and run it:

$ module load nanopolish/0.14.0
$ nanopolish help

Notes from the sysadmin during installation:

$ cd /tmp
$ git clone --recursive https://github.com/jts/nanopolish.git
$ cd nanopolish
$ git checkout v0.14.0
# Load the htslib and minimap2 modules because they provide necessary
# CPPFLAGS and LDFLAGS for the build
$ module load htslib/1.15.1 minimap2/2.24
$ HTS=noinstall MINIMAP2=noinstall make
$ sudo mkdir -p /export/apps/nanopolish/0.14.0
$ sudo chown aorth:aorth /export/apps/nanopolish/0.14.0
$ cp -r bin docs nanopolish test scripts README.md LICENSE /export/apps/nanopolish/0.14.0
$ module load python/3.8
$ python3.8 -m venv /export/apps/nanopolish/0.14.0/venv
$ source /export/apps/nanopolish/0.14.0/venv/bin/activate
$ pip install -r scripts/requirements.txt
$ sudo chown -R root:root /export/apps/nanopolish/0.14.0